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.TH "GMX-TRAJ" "1" "Feb 28, 2024" "2024.1" "GROMACS"
.SH NAME
gmx-traj \- Plot x, v, f, box, temperature and rotational energy from trajectories
.SH SYNOPSIS
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
gmx traj [\fB\-f\fP \fI[<.xtc/.trr/...>]\fP] [\fB\-s\fP \fI[<.tpr/.gro/...>]\fP] [\fB\-n\fP \fI[<.ndx>]\fP]
         [\fB\-ox\fP \fI[<.xvg>]\fP] [\fB\-oxt\fP \fI[<.xtc/.trr/...>]\fP] [\fB\-ov\fP \fI[<.xvg>]\fP]
         [\fB\-of\fP \fI[<.xvg>]\fP] [\fB\-ob\fP \fI[<.xvg>]\fP] [\fB\-ot\fP \fI[<.xvg>]\fP] [\fB\-ekt\fP \fI[<.xvg>]\fP]
         [\fB\-ekr\fP \fI[<.xvg>]\fP] [\fB\-vd\fP \fI[<.xvg>]\fP] [\fB\-cv\fP \fI[<.pdb>]\fP] [\fB\-cf\fP \fI[<.pdb>]\fP]
         [\fB\-av\fP \fI[<.xvg>]\fP] [\fB\-af\fP \fI[<.xvg>]\fP] [\fB\-b\fP \fI<time>\fP] [\fB\-e\fP \fI<time>\fP]
         [\fB\-dt\fP \fI<time>\fP] [\fB\-tu\fP \fI<enum>\fP] [\fB\-[no]w\fP] [\fB\-xvg\fP \fI<enum>\fP] [\fB\-[no]com\fP]
         [\fB\-[no]pbc\fP] [\fB\-[no]mol\fP] [\fB\-[no]nojump\fP] [\fB\-[no]x\fP] [\fB\-[no]y\fP]
         [\fB\-[no]z\fP] [\fB\-ng\fP \fI<int>\fP] [\fB\-[no]len\fP] [\fB\-[no]fp\fP] [\fB\-bin\fP \fI<real>\fP]
         [\fB\-ctime\fP \fI<real>\fP] [\fB\-scale\fP \fI<real>\fP]
.ft P
.fi
.UNINDENT
.UNINDENT
.SH DESCRIPTION
.sp
\fBgmx traj\fP plots coordinates, velocities, forces and/or the box.
With \fB\-com\fP the coordinates, velocities and forces are
calculated for the center of mass of each group.
When \fB\-mol\fP is set, the numbers in the index file are
interpreted as molecule numbers and the same procedure as with
\fB\-com\fP is used for each molecule.
.sp
Option \fB\-ot\fP plots the temperature of each group,
provided velocities are present in the trajectory file.
No corrections are made for constrained degrees of freedom!
This implies \fB\-com\fP\&.
.sp
Options \fB\-ekt\fP and \fB\-ekr\fP plot the translational and
rotational kinetic energy of each group,
provided velocities are present in the trajectory file.
This implies \fB\-com\fP\&.
.sp
Options \fB\-cv\fP and \fB\-cf\fP write the average velocities
and average forces as temperature factors to a \fI\%\&.pdb\fP file with
the average coordinates or the coordinates at \fB\-ctime\fP\&.
The temperature factors are scaled such that the maximum is 10.
The scaling can be changed with the option \fB\-scale\fP\&.
To get the velocities or forces of one
frame set both \fB\-b\fP and \fB\-e\fP to the time of
desired frame. When averaging over frames you might need to use
the \fB\-nojump\fP option to obtain the correct average coordinates.
If you select either of these option the average force and velocity
for each atom are written to an \fI\%\&.xvg\fP file as well
(specified with \fB\-av\fP or \fB\-af\fP).
.sp
Option \fB\-vd\fP computes a velocity distribution, i.e. the
norm of the vector is plotted. In addition in the same graph
the kinetic energy distribution is given.
.sp
See \fI\%gmx trajectory\fP for plotting similar data for selections.
.SH OPTIONS
.sp
Options to specify input files:
.INDENT 0.0
.TP
.B \fB\-f\fP [<.xtc/.trr/...>] (traj.xtc)
Trajectory: \fI\%xtc\fP \fI\%trr\fP \fI\%cpt\fP \fI\%gro\fP \fI\%g96\fP \fI\%pdb\fP \fI\%tng\fP
.TP
.B \fB\-s\fP [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): \fI\%tpr\fP \fI\%gro\fP \fI\%g96\fP \fI\%pdb\fP brk ent
.TP
.B \fB\-n\fP [<.ndx>] (index.ndx) (Optional)
Index file
.UNINDENT
.sp
Options to specify output files:
.INDENT 0.0
.TP
.B \fB\-ox\fP [<.xvg>] (coord.xvg) (Optional)
xvgr/xmgr file
.TP
.B \fB\-oxt\fP [<.xtc/.trr/...>] (coord.xtc) (Optional)
Trajectory: \fI\%xtc\fP \fI\%trr\fP \fI\%cpt\fP \fI\%gro\fP \fI\%g96\fP \fI\%pdb\fP \fI\%tng\fP
.TP
.B \fB\-ov\fP [<.xvg>] (veloc.xvg) (Optional)
xvgr/xmgr file
.TP
.B \fB\-of\fP [<.xvg>] (force.xvg) (Optional)
xvgr/xmgr file
.TP
.B \fB\-ob\fP [<.xvg>] (box.xvg) (Optional)
xvgr/xmgr file
.TP
.B \fB\-ot\fP [<.xvg>] (temp.xvg) (Optional)
xvgr/xmgr file
.TP
.B \fB\-ekt\fP [<.xvg>] (ektrans.xvg) (Optional)
xvgr/xmgr file
.TP
.B \fB\-ekr\fP [<.xvg>] (ekrot.xvg) (Optional)
xvgr/xmgr file
.TP
.B \fB\-vd\fP [<.xvg>] (veldist.xvg) (Optional)
xvgr/xmgr file
.TP
.B \fB\-cv\fP [<.pdb>] (veloc.pdb) (Optional)
Protein data bank file
.TP
.B \fB\-cf\fP [<.pdb>] (force.pdb) (Optional)
Protein data bank file
.TP
.B \fB\-av\fP [<.xvg>] (all_veloc.xvg) (Optional)
xvgr/xmgr file
.TP
.B \fB\-af\fP [<.xvg>] (all_force.xvg) (Optional)
xvgr/xmgr file
.UNINDENT
.sp
Other options:
.INDENT 0.0
.TP
.B \fB\-b\fP <time> (0)
Time of first frame to read from trajectory (default unit ps)
.TP
.B \fB\-e\fP <time> (0)
Time of last frame to read from trajectory (default unit ps)
.TP
.B \fB\-dt\fP <time> (0)
Only use frame when t MOD dt = first time (default unit ps)
.TP
.B \fB\-tu\fP <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s
.TP
.B \fB\-[no]w\fP  (no)
View output \fI\%\&.xvg\fP, \fI\%\&.xpm\fP, \fI\%\&.eps\fP and \fI\%\&.pdb\fP files
.TP
.B \fB\-xvg\fP <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
.TP
.B \fB\-[no]com\fP  (no)
Plot data for the com of each group
.TP
.B \fB\-[no]pbc\fP  (yes)
Make molecules whole for COM
.TP
.B \fB\-[no]mol\fP  (no)
Index contains molecule numbers instead of atom numbers
.TP
.B \fB\-[no]nojump\fP  (no)
Remove jumps of atoms across the box
.TP
.B \fB\-[no]x\fP  (yes)
Plot X\-component
.TP
.B \fB\-[no]y\fP  (yes)
Plot Y\-component
.TP
.B \fB\-[no]z\fP  (yes)
Plot Z\-component
.TP
.B \fB\-ng\fP <int> (1)
Number of groups to consider
.TP
.B \fB\-[no]len\fP  (no)
Plot vector length
.TP
.B \fB\-[no]fp\fP  (no)
Full precision output
.TP
.B \fB\-bin\fP <real> (1)
Binwidth for velocity histogram (nm/ps)
.TP
.B \fB\-ctime\fP <real> (\-1)
Use frame at this time for x in \fB\-cv\fP and \fB\-cf\fP instead of the average x
.TP
.B \fB\-scale\fP <real> (0)
Scale factor for \fI\%\&.pdb\fP output, 0 is autoscale
.UNINDENT
.SH SEE ALSO
.sp
\fBgmx(1)\fP
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2024, GROMACS development team
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